The history of leprosy and its interaction with man is one of suffering and misunderstanding. The newest research suggests that at least as early as 4000 B.C. individuals had been infected with M. leprae, while the first known written reference to the disease was found on Egyptian papyrus in about 1550 B.C. It is a chronic infectious disease afflicting between 10 and 15 million people, is caused by the obligate intracellular parasite Mycobacterium leprae. It causes damage to the skin and the peripheral nervous system. The disease develops slowly and results in skin lesions and deformities, most often affecting the cooler places on the body such as eyes, nose, earlobes, hands, feet, and testicles. The skin lesions and deformities can be very disfiguring and are the reason that infected individuals historically were considered outcasts in many cultures. Although human-to-human transmission is the primary source of infection, three other species can carry and (rarely) transfer M. leprae to humans: chimpanzees, mangabey monkeys, and nine-banded armadillos.
Leprosy is caused mainly by Mycobacterium leprae, a rod-shaped bacillus that is an obligate intracellular (only grows inside of certain human and animal cells) bacterium. The early signs and symptoms of leprosy are very subtle and occur slowly. Numbness and loss of temperature sensation are some of the first symptoms that patients experience. As the disease progresses, the sensations of touch, then pain, and eventually deep pressure are decreased or lost.
The protein selected for pharmacophore studies and structure based drug designing is serine hydroxymethyltransferase. Enzyme commission (E.C) number of the 220.127.116.11. and the sequence length is 426aa. Gene name for the protein is glyA. The main function of serine hydroxymethyltransferase is the interconversion of serine and glycine.
MATERIALS AND METHODS
Materials required for the further proceeding of the project work includes information collection regarding the protein sequence (SHMT) in FASTA format from the SwissProt database and the Protein Information Resource (PIR) database, relevant literature support from the PubMed database, metabolic pathway information of the protein from the KEGG pathway database and selection of ligand molecules from the DrugBank database in SMILES notation.
The entire project work was performed with the help of Accelrys Discovery Studio 2.5 and using various tools present within the software. The list of tools being used during the project work can be mentioned as such:
1. For sequence alignment the tool "BLAST search (NCBI server)" was used.
2. The tool "Align Sequence to Template" was being used for the alignment of the protein target sequence to the template sequence.
3. For modeling of the protein sequence (SHMT) with reference to the template sequence, the tool "Build Homology Models" was used.
4. The verification of the protein 3D structure was done by using the the tool "Verify Protein (Profiles-3D)".
5. For common pharmacophore studies of both the ligand and the receptor molecule, the tool "Common Feature Pharmacophore" was being used and for searching of ligands with common pharmacophore, the tool "Search 3D Database" was used.
6. Two tools namely "ADMET Descriptors" and "Toxicity Prediction (TOPKAT)" under the protocol "ADMET" was being used to check whether the ligand molecules satisfies all the required properties for receptor-ligand interaction such as "Aqueous solubility", "Blood brain barrier penetration(BBB)", "Cytochrome P450 (CYP450) 2D6 inhibition", "Hepatotoxicity", "Human intestinal absorption (HIA)", and "Plasma protein binding" and to check whether the ligand molecule is toxic under any condition before binding to the receptor molecule, if so we can easily sort out that specific ligand molecule before further proceeding.
7. The protein receptor molecule has to be optimized before binding to the ligand molecule. For doing so, the receptor molecule has to be stimulated for the generation of force field "CHARMm", and then specifying the active sites for binding of the ligand molecule by using the tool "Receptor-Ligand Interaction".
8. Finally, docking of the receptor to the ligand molecule is done by using the tool "Dock Ligands (LigandFit)" which is based upon the "Ligand Fit" algorithm.
The results of the project work can be summurised in the following way:
Sequence analysis of the target protein through the BLAST server returned with 41 hits, out of which, the sequence 3H7F which has a sequence length of 447aa, with 89% identity and 93% positive was selected as the template sequence for homology modeling of the unstructured protein serine hydroxymethyltransferase (SHMT). Three homology models of the protein SHMT was modeled, out of which, the model with a DOPE score of -46959.18 was selected for further studies. The DOPE score gives the structural stability of the protein structure. A low DOPE score indicates for a better stability of the 3D structure. For binding of the receptor to ligand molecules, the ligand molecules were scanned for pharmacophore regions common to both the receptor and the ligand. The ADMET results shows that only two amino acids falls out of the graph region. These two amino acid comes outside of the domain region of the protein. The domain region of the protein starts from 26 to 419, and that the two amino acids lies in the region of 119 and 430. Since all the amino acids comes under the domain region so no energy minimization was performed. Toxicity prediction of the ligand BTB03887 on male rat, female rat, male mouse, female mouse and ames mutagenicity shows no carcinogenicity. This shows that the ligand molecule can be considered for docking process.
Fig 1. Active site "Site1"
The above given figure shows the active site "Site 1" for binding of the ligand BTB03887 to the receptor molecule.
Finally, docking of the ligand and the receptor molecule was done by using the Dock Ligands (LigandFit) tool. A snapshot of the docked receptor and ligand molecule is shown.
Fig 2. Result for the docked molecule
The above figure shows the distance between between that are bonded. Distance between the atoms H34 and O is 1.760. Distance between the atoms H31 and O is 2.325. The overall dock score gives a value of 51.443.
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